烟草科技2018，Vol.51Issue(1)：8-14,7.DOI:10.16135/j.issn1002-0861.2017.0189
群体遗传变异鉴定工具系统比较
Systematic comparison of population genetic variation calling tools
摘要
Abstract
To select suitable population genetic variation calling tools for various datasets, different software tools (samtools, gatk, freebayes and sambamba) were compared. The variations were extracted from resequencing datasets, including three species (Arabidopsis, rice and human) with different genome sizes and tobacco linkage group 1, by different tools. The comparison results of single-sample and multiple-sample data showed that samtools and sambamba tended to produce as much as variations, whereas outputs from gatk and freebayes tended to contain higher accuracy variations. Sambamba was much faster than the other tools, and gatk had some advantages in speed for multiple-sample data analysis. Gatk consumed much more computing memory than the other tools.关键词
下一代测序/重测序/群体遗传变异/系统比较Key words
Next generation sequencing/Resequencing/Population genetic variation/Systematic comparison分类
生物科学引用本文复制引用
李泽锋,卢鹏,张剑锋,张慧,许亚龙,金静静..群体遗传变异鉴定工具系统比较[J].烟草科技,2018,51(1):8-14,7.基金项目
中国烟草总公司郑州烟草研究院院长科技发展基金项目"群体遗传变异鉴定并行化算法开发与实现"(902015CA0250). （902015CA0250）
